Autonomous circadian rhythms in the human hepatocyte regulate hepatic drug metabolism and inflammatory responses

Critical aspects of physiology and cell function exhibit self-sustained ~24-hour variations termed circadian rhythms. In the liver, circadian rhythms play fundamental roles in maintaining organ homeostasis. Here, we established and characterized an in vitro liver experimental system in which primary human hepatocytes display self-sustained oscillations. By generating gene expression profiles of these hepatocytes over time, we demonstrated that their transcriptional state is dynamic across 24 hours and identified a set of cycling genes with functions related to inflammation, drug metabolism, and energy homeostasis. We designed and tested a treatment protocol to minimize atorvastatin- and acetaminophen-induced hepatotoxicity. Last, we documented circadian-dependent induction of pro-inflammatory cytokines when triggered by LPS, IFN-β, or Plasmodium infection in human hepatocytes. Collectively, our findings emphasize that the phase of the circadian cycle has a robust impact on the efficacy and toxicity of drugs, and we provide a test bed to study the timing and magnitude of inflammatory responses over the course of infection in human liver.

Scalable Surveillance of E-Cigarette Products on Instagram and TikTok Using Computer Vision

INTRODUCTION

Instagram and TikTok, video-based social media platforms popular among adolescents, contain tobacco-related content despite the platforms' policies prohibiting substance-related posts. Prior research identified themes in e-cigarette-related social media posts using qualitative or text-based machine learning methods. We developed an image-based computer vision model to identify e-cigarette products in social media images and videos.

AIMS AND METHODS

We created a data set of 6999 Instagram images labeled for 8 object classes: mod or pod devices, e-juice containers, packaging boxes, nicotine warning labels, e-juice flavors, e-cigarette brand names, and smoke clouds. We trained a DyHead object detection model using a Swin-Large backbone, evaluated the model's performance on 20 Instagram and TikTok videos, and applied the model to 14 072 e-cigarette-related promotional TikTok videos (2019-2022; 10 276 485 frames).

RESULTS

The model achieved the following mean average precision scores on the image test set: e-juice container: 0.89; pod device: 0.67; mod device: 0.54; packaging box: 0.84; nicotine warning label: 0.86; e-cigarette brand name: 0.71; e-juice flavor name: 0.89; and smoke cloud: 0.46. The prevalence of pod devices in promotional TikTok videos increased by 15% from 2019 to 2022. The prevalence of e-juices increased by 33% from 2021 to 2022. The prevalence of e-juice flavor names and e-cigarette brand names increased by about 100% from 2019 to 2022.

CONCLUSIONS

Deep learning-based object detection technology enables automated analysis of visual posts on social media. Our computer vision model can detect the presence of e-cigarettes products in images and videos, providing valuable surveillance data for tobacco regulatory science (TRS).

IMPLICATIONS

Prior research identified themes in e-cigarette-related social media posts using qualitative or text-based machine learning methods. We developed an image-based computer vision model to identify e-cigarette products in social media images and videos. We trained a DyHead object detection model using a Swin-Large backbone, evaluated the model's performance on 20 Instagram and TikTok videos featuring at least two e-cigarette objects, and applied the model to 14 072 e-cigarette-related promotional TikTok videos (2019-2022; 10 276 485 frames). The deep learning model can be used for automated, scalable surveillance of image- and video-based e-cigarette-related promotional content on social media, providing valuable data for TRS. Social media platforms could use computer vision to identify tobacco-related imagery and remove it promptly, which could reduce adolescents' exposure to tobacco content online.

Breast Radiologists' Perceptions on the Detection and Management of Invasive Lobular Carcinoma: Most Agree Imaging Beyond Mammography Is Warranted

OBJECTIVE

To determine breast radiologists' confidence in detecting invasive lobular carcinoma (ILC) on mammography and the perceived need for additional imaging in screening and preoperative settings.

METHODS

A 16-item anonymized survey was developed, and IRB exemption obtained, by the Society of Breast Imaging (SBI) Patient Care and Delivery Committee and the Lobular Breast Cancer Alliance. The survey was emailed to 2946 radiologist SBI members on February 15, 2023. The survey recorded demographics, perceived modality-specific sensitivity for ILC to the nearest decile, and opinions on diagnosing ILC in screening and staging imaging. Five-point Likert scales were used (1 = strongly disagree, 2 = disagree, 3 = neutral, 4 = agree, 5 = strongly agree).

RESULTS

Response rate was 12.4% (366/2946). Perceived median (interquartile range) modality-specific sensitivities for ILC were MRI 90% (80-90), contrast-enhanced mammography 80% (70-90), molecular breast imaging 80% (60-90), digital breast tomosynthesis 70% (60-80), US 60% (50-80), and 2D mammography 50% (30-60). Only 25% (85/340) respondents were confident in detecting ILC on screening mammography in dense breasts, while 67% (229/343) were confident if breasts were nondense. Most agreed that supplemental screening is needed to detect ILC in women with dense breasts (272/344, 79%) or a personal history of ILC (248/341, 73%), with 34% (118/334) indicating that supplemental screening would also benefit women with nondense breasts. Most agreed that additional imaging is needed to evaluate extent of disease in women with newly diagnosed ILC, regardless of breast density (dense 320/329, 97%; nondense 263/329, 80%).

CONCLUSION

Most breast radiologists felt that additional imaging beyond mammography is needed to more confidently screen for and stage ILC.

Characterizing Mobility and its Association with HIV Outcomes in Refugee Settlements in Uganda

Background

A better understanding of refugee mobility is needed to optimize HIV care in refugee settlements.

Objectives

We aimed to characterize mobility patterns among people living with HIV in refugee settlements in Uganda and evaluate the association between mobility and retention in HIV care.

Methods

Refugees and Ugandan nationals accessing HIV services at seven health centers in refugee settlements across Uganda, with access to a phone, were recruited and followed for six months. Participants received an intake survey and monthly phone surveys on mobility and HIV. Clinic visit and viral suppression data were extracted from clinic registers. Mobility and HIV data were presented descriptively, and an alluvial plot was generated characterizing mobility for participants' most recent trip. Bivariate Poisson regression models were used to describe the associations between long-term mobility (≥1 continuous month away in the past year) and demographic characteristics, retention (≥1 clinic visit/6 months) and long-term mobility, and retention and general mobility (during any follow-up month: ≥2 trips, travel outside the district or further, or spending >1-2 weeks (8-14 nights) away).

Findings

Mobility data were provided by 479 participants. At baseline, 67 participants (14%) were considered long-term mobile. Male sex was associated with an increased probability of long-term mobility (RR 2.02; 95%CI: 1.30-3.14, p < 0.01). In follow-up, 185 participants (60% of respondents) were considered generally mobile. Reasons for travel included obtaining food or supporting farming activities (45% of trips) and work or trade (33% of trips). Retention in HIV care was found for 417 (87%) participants. Long-term mobility was associated with a 14% (RR 0.86; 95%CI: 0.75-0.98) lower likelihood of retention (p = 0.03).

Conclusions

Refugees and Ugandan nationals accessing HIV care in refugee settlements frequently travel to support their survival needs. Mobility is associated with inferior retention and should be considered in interventions to optimize HIV care.

Protein biomarkers and alternatively methylated cell-free DNA detect early stage pancreatic cancer

OBJECTIVE

Pancreatic ductal adenocarcinoma (PDAC) is commonly diagnosed at an advanced stage. Liquid biopsy approaches may facilitate detection of early stage PDAC when curative treatments can be employed.

DESIGN

To assess circulating marker discrimination in training, testing and validation patient cohorts (total n=426 patients), plasma markers were measured among PDAC cases and patients with chronic pancreatitis, colorectal cancer (CRC), and healthy controls. Using CA19-9 as an anchor marker, measurements were made of two protein markers (TIMP1, LRG1) and cell-free DNA (cfDNA) pancreas-specific methylation at 9 loci encompassing 61 CpG sites.

RESULTS

Comparative methylome analysis identified nine loci that were differentially methylated in exocrine pancreas DNA. In the training set (n=124 patients), cfDNA methylation markers distinguished PDAC from healthy and CRC controls. In the testing set of 86 early stage PDAC and 86 matched healthy controls, CA19-9 had an area under the receiver operating characteristic curve (AUC) of 0.88 (95% CI 0.83 to 0.94), which was increased by adding TIMP1 (AUC 0.92; 95% CI 0.88 to 0.96; p=0.06), LRG1 (AUC 0.92; 95% CI 0.88 to 0.96; p=0.02) or exocrine pancreas-specific cfDNA methylation markers at nine loci (AUC 0.92; 95% CI 0.88 to 0.96; p=0.02). In the validation set of 40 early stage PDAC and 40 matched healthy controls, a combined panel including CA19-9, TIMP1 and a 9-loci cfDNA methylation panel had greater discrimination (AUC 0.86, 95% CI 0.77 to 0.95) than CA19-9 alone (AUC 0.82; 95% CI 0.72 to 0.92).

CONCLUSION

A combined panel of circulating markers including proteins and methylated cfDNA increased discrimination compared with CA19-9 alone for early stage PDAC.

Exposure to polycyclic aromatic hydrocarbons, volatile organic compounds, and tobacco-specific nitrosamines and incidence of esophageal cancer

BACKGROUND

Studying carcinogens in tobacco and nontobacco sources may be key to understanding the pathogenesis and geographic distribution of esophageal cancer.

METHODS

The Golestan Cohort Study has been conducted since 2004 in a region with high rates of esophageal squamous cell carcinoma. For this nested study, the cases comprised of all incident cases by January 1, 2018; controls were matched to the case by age, sex, residence, time in cohort, and tobacco use. We measured urinary concentrations of 33 exposure biomarkers of nicotine, polycyclic aromatic hydrocarbons, volatile organic compounds, and tobacco-specific nitrosamines. We used conditional logistic regression to calculate odds ratios (ORs) and 95% confidence intervals for associations between the 90th vs the 10th percentiles of the biomarker concentrations and incident esophageal squamous cell carcinoma.

RESULTS

Among individuals who did not currently use tobacco (148 cases and 163 controls), 2 acrolein metabolites, 2 acrylonitrile metabolites, 1 propylene oxide metabolite, and one 1,3-butadiene metabolite were significantly associated with incident esophageal squamous cell carcinoma (adjusted odds ratios between 1.8 and 4.3). Among tobacco users (57 cases and 63 controls), metabolites of 2 other volatile organic compounds (styrene and xylene) were associated with esophageal squamous cell carcinoma (OR = 6.2 and 9.0, respectively). In tobacco users, 2 tobacco-specific nitrosamines (NNN and N'-Nitrosoanatabine) were also associated with esophageal squamous cell carcinoma. Suggestive associations were seen with some polycyclic aromatic hydrocarbons (especially 2-hydroxynaphthalene) in nonusers of tobacco products and other tobacco-specific nitrosamines in tobacco users.

CONCLUSION

These novel associations based on individual-level data and samples collected many years before cancer diagnosis, from a population without occupational exposure, have important public health implications.

Efficacy of Single-Agent Chemotherapy in Endocrine Therapy-Refractory Metastatic Invasive Lobular Carcinoma

BACKGROUND

Hormone receptor (HR)-positive, HER2-negative metastatic invasive lobular breast cancer (mILC) is distinct from invasive ductal cancer (IDC) in clinicopathologic and molecular characteristics, impacting its response to systemic therapy. While endocrine therapy (ET) combined with targeted therapies has shown efficacy in ET-sensitive mILC, data on chemotherapy in ET-refractory mILC remain limited. We investigated the efficacy of single-agent capecitabine (CAP) versus taxanes (TAX) in ET-refractory HR+ HER2-negative patients with mILC.

MATERIALS AND METHODS

Using data from the MD Anderson prospectively collected breast cancer database, we identified patients with HR+ HER2-negative mILC who received prior ET and first-time chemotherapy in the metastatic setting. We compared outcomes between 173 CAP-treated and 96 TAX-treated patients.

RESULTS

CAP-treated patients had significantly better median progression-free survival (PFS) than TAX-treated patients (8.8 vs 5.0 months, HR 0.63, P < .001). Overall survival (OS) did not differ significantly between the groups (42.7 vs 36.6 months for CAP vs TAX, respectively, HR 0.84, P = .241). Multivariate analyses for PFS and OS revealed better outcomes in subjects with fewer metastatic sites and those exposed to more lines of ET. Additionally, Black patients showed worse OS outcomes compared to White patients (HR 2.46; P = .001).

CONCLUSION

In ET-refractory HR+ HER2-negative mILC, single-agent CAP demonstrated superior PFS compared to TAX. Our findings highlight the potential benefit of CAP in this patient subset, warranting further investigation through prospective trials.

Integrating multi-modal imaging in radiation treatments for glioblastoma

Advances in diagnostic and treatment technology along with rapid developments in translational research may now allow the realization of precision radiotherapy. Integration of biologically informed multimodality imaging to address the spatial and temporal heterogeneity underlying treatment resistance in glioblastoma is now possible for patient care, with evidence of safety and potential benefit. Beyond their diagnostic utility, several candidate imaging biomarkers have emerged in recent early-phase clinical trials of biologically based radiotherapy, and their definitive assessment in multicenter prospective trials is already in development. In this review, the rationale for clinical implementation of candidate advanced magnetic resonance imaging and positron emission tomography imaging biomarkers to guide personalized radiotherapy, the current landscape, and future directions for integrating imaging biomarkers into radiotherapy for glioblastoma are summarized. Moving forward, response-adaptive radiotherapy using biologically informed imaging biomarkers to address emerging treatment resistance in rational combination with novel systemic therapies may ultimately permit improvements in glioblastoma outcomes and true individualization of patient care.

SAMHD1 expression contributes to doxorubicin resistance and predicts survival outcomes in diffuse large B-cell lymphoma patients

Diffuse large B-cell lymphoma (DLBCL) is a commonly diagnosed, aggressive non-Hodgkin's lymphoma. While R-CHOP chemoimmunotherapy is potentially curative, about 40% of DLBCL patients will fail, highlighting the need to identify biomarkers to optimize management. SAMHD1 has a dNTPase-independent role in promoting resection to facilitate DNA double-strand break (DSB) repair by homologous recombination. We evaluated the relationship of SAMHD1 levels with sensitivity to DSB-sensitizing agents in DLBCL cells and the association of SAMHD1 expression with clinical outcomes in 79 DLBCL patients treated with definitive therapy and an independent cohort dataset of 234 DLBCL patients. Low SAMHD1 expression, Vpx-mediated, or siRNA-mediated degradation/depletion in DLBCL cells was associated with greater sensitivity to doxorubicin and PARP inhibitors. On Kaplan-Meier log-rank survival analysis, low SAMHD1 expression was associated with improved overall survival (OS), which on subset analysis remained significant only in patients with advanced stage (III-IV) and moderate to high risk (2-5 International Prognostic Index (IPI)). The association of low SAMHD1 expression with improved OS remained significant on multivariate analysis independent of other adverse factors, including IPI, and was validated in an independent cohort. Our findings suggest that SAMHD1 expression mediates doxorubicin resistance and may be an important prognostic biomarker in advanced, higher-risk DLBCL patients.

Retinoic acid receptor α activity in proximal tubules prevents kidney injury and fibrosis

Chronic kidney disease (CKD) is characterized by a gradual loss of kidney function and affects ~13.4% of the global population. Progressive tubulointerstitial fibrosis, driven in part by proximal tubule (PT) damage, is a hallmark of late stages of CKD and contributes to the development of kidney failure, for which there are limited treatment options. Normal kidney development requires signaling by vitamin A (retinol), which is metabolized to retinoic acid (RA), an endogenous agonist for the RA receptors (RARα, β, γ). RARα levels are decreased in a mouse model of diabetic nephropathy and restored with RA administration; additionally, RA treatment reduced fibrosis. We developed a mouse model in which a spatiotemporal (tamoxifen-inducible) deletion of RARα in kidney PT cells of adult mice causes mitochondrial dysfunction, massive PT injury, and apoptosis without the use of additional nephrotoxic substances. Long-term effects (3 to 4.5 mo) of RARα deletion include increased PT secretion of transforming growth factor β1, inflammation, interstitial fibrosis, and decreased kidney function, all of which are major features of human CKD. Therefore, RARα's actions in PTs are crucial for PT homeostasis, and loss of RARα causes injury and a key CKD phenotype.

Harvest for health in survivors of chronic disease: A demonstration project in the Alabama Black Belt and Mississippi Delta Region

This demonstration project expands upon the Harvest for Health vegetable gardening intervention for cancer survivors by: (i) including survivors of other chronic diseases (i.e. heart disease and diabetes); and (ii) targeting an area with known health inequities (Alabama Black Belt and Mississippi Delta Region). To assess: (i) gardening acceptability (engagement, satisfaction, sustainability, and safety); and (ii) changes over time in health behaviors (fruit and vegetable [F&V] intake, and physical activity) and outcomes (physical performance and anthropometrics). Chronic disease survivors (CDS) were recruited across 15 counties in Alabama and Mississippi and provided with gardening supplies and paired with a master gardener (MG). MGs mentored participants in planning, planting, and maintaining a vegetable garden over a 3-month period. Data collection consisted of an electronic survey (baseline, post-intervention, 6-month follow-up) and community-based physical assessments (baseline and post-intervention). Participants (n = 137; 92% African American; Mage = 65) included individuals with a history of diabetes (56%), heart disease (29%), and cancer (26%). Seventy-five percent of participants engaged in gardening ≥3 times a week. Significant improvements in F&V intake (+0.73, P = .04), physical activity (+49.6, P < .01), and 4 of 7 physical performance measures were observed, while positive trends were seen in others. Eighteen participants withdrew (13% attrition rate). No adverse events occurred. Participants were satisfied with their gardening experience (90%) and were still gardening at 6-month follow-up (85%). Seventy-two percent of participants expanded, or planned on expanding, their garden at 6-month follow-up. Harvest for Health was acceptable and associated with improved health behaviors and outcomes.

Metastatic gastric cancer target lesion complete response with Claudin18.2-CAR T cells

Treatment of hematologic malignancies with patient-derived anti-CD19 chimeric antigen receptor (CAR) T-cells has demonstrated long-term remissions for patients with otherwise treatment-refractory advanced leukemia and lymphoma. Conversely, CAR T-cell treatment of solid tumors, including advanced gastric cancer (GC), has proven more challenging due to on-target off-tumor toxicities, poor tumor T-cell infiltration, inefficient CAR T-cell expansion, immunosuppressive tumor microenvironments, and demanding preconditioning regimens. We report the exceptional results of autologous Claudin18.2-targeted CAR T cells (CT041) in a patient with metastatic GC, who had progressed on four lines of combined systemic chemotherapy and immunotherapy. After two CT041 infusions, the patient had target lesion complete response and sustained an 8-month overall partial response with only minimal ascites. Moreover, tumor-informed circulating tumor DNA (ctDNA) reductions coincided with rapid CAR T-cell expansion and radiologic response. No severe toxicities occurred, and the patient's quality of life significantly improved. This experience supports targeting Claudin18.2-positive GC with CAR T-cell therapy and helps to validate ctDNA as a biomarker in CAR T-cell therapy. Clinical Insight: Claudin18.2-targeted CAR T cells can safely provide complete objective and ctDNA response in salvage metastatic GC.

Distinct senescence mechanisms restrain progression of dysplastic nevi

Telomerase reverse transcriptase (TERT) promoter mutations (TPMs) are frequently found in different cancer types, including ∼70% of sun-exposed skin melanomas. In melanoma, TPMs are among the earliest mutations and can be present during the transition from nevus to melanoma. However, the specific factors that contribute to the selection of TPMs in certain nevi subsets are not well understood. To investigate this, we analyzed a group of dysplastic nevi (DN) by sequencing genes commonly mutated in melanocytic neoplasms. We examined the relationship between the identified mutations, patient age, telomere length, histological features, and the expression of p16. Our findings reveal that TPMs are more prevalent in DN from older patients and are associated with shorter telomeres. Importantly, these TPMs were not found in nevi with BRAF V600E mutations. Conversely, DN with BRAF V600E mutations were observed in younger patients, had longer telomeres and a higher proportion of p16-positive cells. This suggests that these nevi arrest growth independently of telomere shortening through a mechanism known as oncogene-induced senescence (OIS). These characteristics extend to melanoma-sequencing datasets, where melanomas with BRAF V600E mutations were more likely to have a CDKN2A inactivation, overriding OIS. In contrast, melanomas without BRAF V600E mutations showed a higher frequency of TPMs. Our data imply that TPMs are selected to bypass replicative senescence (RS) in cells that were not arrested by OIS. Overall, our results indicate that a subset of melanocytic neoplasms face constraints from RS, while others encounter OIS and RS. The order in which these barriers are overcome during progression to melanoma depends on the mutational context.

The Third Annual Symposium of the Midwest Aging Consortium

The geroscience hypothesis suggests that addressing the fundamental mechanisms driving aging biology will prevent or mitigate the onset of multiple chronic diseases, for which the largest risk factor is advanced age. Research that investigates the root causes of aging is therefore of critical importance given the rising healthcare burden attributable to age-related diseases. The third annual Midwest Aging Consortium symposium was convened as a showcase of such research performed by investigators from institutions across the Midwestern United States. This report summarizes the work presented during a virtual conference across topics in aging biology, including immune function in the lung-particularly timely given the Corona Virus Immune Disease-2019 pandemic-along with the role of metabolism and nutrient-regulated pathways in cellular function with age, the influence of senescence on stem cell function and inflammation, and our evolving understanding of the mechanisms underlying observation of sex dimorphism in aging-related outcomes. The symposium focused on early-stage and emerging investigators, while including keynote presentations from leaders in the biology of aging field, highlighting the diversity and strength of aging research in the Midwest.

Atomic diffusion and mixing in old stars - VIII. Chemical abundance variations in the globular cluster M4 (NGC 6121)

Variations in chemical abundances with evolutionary phase have been identified among stars in globular and open clusters with a wide range of metallicities. In the metal-poor clusters, these variations compare well with predictions from stellar structure and evolution models considering the internal diffusive motions of atoms and ions, collectively known as atomic diffusion, when moderated by an additional mixing process with a fine-tuned efficiency. We present here an investigation of these effects in the Galactic globular cluster NGC 6121 (M4) ([Fe/H] = -1.13) through a detailed chemical abundance analysis of 86 stars using high-resolution ESO Very Large Telescope (VLT) Fibre Large Array Multi Element Spectrograph (FLAMES) spectroscopy. The stars range from the main-sequence turnoff point (TOP) to the red giant branch (RGB) just above the bump. We identify C-N-O and Mg-Al-Si abundance anticorrelations, and confirm the presence of a bimodal population differing by 1 dex in nitrogen abundance. The composition of the second-generation stars imply pollution from both massive (20-40 [Formula: see text]) and asymptotic giant branch stars. We find evolutionary variations in chemical abundances between the TOP and RGB, which are robust to uncertainties in stellar parameters and modelling assumptions. The variations are weak, but match predictions well when employing efficient additional mixing. Without correcting for Galactic production of lithium, we derive an initial lithium abundance 2.63 ± 0.10, which is marginally lower than the predicted primordial big-bang nucleosynthesis value.

Patient-derived organoids recapitulate glioma-intrinsic immune program and progenitor populations of glioblastoma

Glioblastoma multiforme (GBM) is a highly lethal human cancer thought to originate from a self-renewing and therapeutically-resistant population of glioblastoma stem cells (GSCs). The intrinsic mechanisms enacted by GSCs during 3D tumor formation, however, remain unclear, especially in the stages prior to angiogenic/immunological infiltration. In this study, we performed a deep characterization of the genetic, immune, and metabolic profiles of GBM organoids from several patient-derived GSCs (GBMO). Despite being devoid of immune cells, transcriptomic analysis across GBMO revealed a surprising immune-like molecular program, enriched in cytokine, antigen presentation and processing, T-cell receptor inhibitors, and interferon genes. We find two important cell populations thought to drive GBM progression, Special AT-rich sequence-binding protein 2 (SATB2+) and homeodomain-only protein homeobox (HOPX+) progenitors, contribute to this immune landscape in GBMO and GBM in vivo. These progenitors, but not other cell types in GBMO, are resistant to conventional GBM therapies, temozolomide and irradiation. Our work defines a novel intrinsic immune-like landscape in GBMO driven, in part, by SATB2+ and HOPX+ progenitors and deepens our understanding of the intrinsic mechanisms utilized by GSCs in early GBM formation.

Induced degradation of lineage-specific oncoproteins drives the therapeutic vulnerability of small cell lung cancer to PARP inhibitors

Although BRCA1/2 mutations are not commonly found in small cell lung cancer (SCLC), a substantial fraction of SCLC shows clinically relevant response to PARP inhibitors (PARPis). However, the underlying mechanism(s) of PARPi sensitivity in SCLC is poorly understood. We performed quantitative proteomic analyses and identified proteomic changes that signify PARPi responses in SCLC cells. We found that the vulnerability of SCLC to PARPi could be explained by the degradation of lineage-specific oncoproteins (e.g., ASCL1). PARPi-induced activation of the E3 ligase HUWE1 mediated the ubiquitin-proteasome system (UPS)-dependent ASCL1 degradation. Although PARPi induced a general DNA damage response in SCLC cells, this signal generated a cell-specific response in ASCL1 degradation, leading to the identification of HUWE1 expression as a predictive biomarker for PARPi. Combining PARPi with agents targeting these pathways markedly improved therapeutic response in SCLC. The degradation of lineage-specific oncoproteins therefore represents a previously unidentified mechanism for PARPi efficacy in SCLC.

Molecular features of prostate cancer after neoadjuvant therapy in the phase 3 CALGB 90203 trial

BACKGROUND

The phase 3 CALGB 90203 (Alliance) trial evaluated neoadjuvant chemohormonal therapy for high-risk localized prostate cancer before radical prostatectomy. We dissected the molecular features of post-treated tumors with long-term clinical outcomes to explore mechanisms of response and resistance to chemohormonal therapy.

METHODS

We evaluated 471 radical prostatectomy tumors, including 294 samples from 166 patients treated with 6 cycles of docetaxel plus androgen deprivation therapy before radical prostatectomy and 177 samples from 97 patients in the control arm (radical prostatectomy alone). Targeted DNA sequencing and RNA expression of tumor foci and adjacent noncancer regions were analyzed in conjunction with pathologic changes and clinical outcomes.

RESULTS

Tumor fraction estimated from DNA sequencing was significantly lower in post-treated tumor tissues after chemohormonal therapy compared with controls. Higher tumor fraction after chemohormonal therapy was associated with aggressive pathologic features and poor outcomes, including prostate-specific antigen-progression-free survival. SPOP alterations were infrequently detected after chemohormonal therapy, while TP53 alterations were enriched and associated with shorter overall survival. Residual tumor fraction after chemohormonal therapy was linked to higher expression of androgen receptor-regulated genes, cell cycle genes, and neuroendocrine genes, suggesting persistent populations of active prostate cancer cells. Supervised clustering of post-treated high-tumor-fraction tissues identified a group of patients with elevated cell cycle-related gene expression and poor clinical outcomes.

CONCLUSIONS

Distinct recurrent prostate cancer genomic and transcriptomic features are observed after exposure to docetaxel and androgen deprivation therapy. Tumor fraction assessed by DNA sequencing quantifies pathologic response and could be a useful trial endpoint or prognostic biomarker. TP53 alterations and high cell cycle transcriptomic activity are linked to aggressive residual disease, despite potent chemohormonal therapy.

Poor oral health influences head and neck cancer patient survival: an International Head and Neck Cancer Epidemiology Consortium pooled analysis

BACKGROUND

Poor oral health has been identified as a prognostic factor potentially affecting the survival of patients with head and neck squamous cell carcinoma. However, evidence to date supporting this association has emanated from studies based on single cohorts with small-to-modest sample sizes.

METHODS

Pooled analysis of 2449 head and neck squamous cell carcinoma participants from 4 studies of the International Head and Neck Cancer Epidemiology Consortium included data on periodontal disease, tooth brushing frequency, mouthwash use, numbers of natural teeth, and dental visits over the 10 years prior to diagnosis. Multivariable generalized linear regression models were used and adjusted for age, sex, race, geographic region, tumor site, tumor-node-metastasis stage, treatment modality, education, and smoking to estimate risk ratios (RR) of associations between measures of oral health and overall survival.

RESULTS

Remaining natural teeth (10-19 teeth: RR = 0.81, 95% confidence interval [CI] = 0.69 to 0.95; ≥20 teeth: RR = 0.88, 95% CI = 0.78 to 0.99) and frequent dental visits (>5 visits: RR = 0.77, 95% CI = 0.66 to 0.91) were associated with better overall survival. The inverse association with natural teeth was most pronounced among patients with hypopharyngeal and/or laryngeal, and not otherwise specified head and neck squamous cell carcinoma. The association with dental visits was most pronounced among patients with oropharyngeal head and neck squamous cell carcinoma. Patient-reported gingival bleeding, tooth brushing, and report of ever use of mouthwash were not associated with overall survival.

CONCLUSIONS

Good oral health as defined by maintenance of the natural dentition and frequent dental visits appears to be associated with improved overall survival among head and neck squamous cell carcinoma patients.

Contemporary Prophylactic Antibiotic Practices and Adjunct Therapies in Autologous Fat Grafting Procedures: A Survey of The Aesthetic Society Members

Background

Autologous fat grafting (AFG) is a widely used surgical technique that involves extracting a patient's own adipose tissue and transferring it to different areas of the body. This practice is still evolving. Guidelines for antibiotic prophylaxis and use of adjuncts in plastic surgery are currently limited, with a notable absence of standardized guidelines for AFG.

Objectives

In this survey, we assess contemporary antibiotic practices and adjuncts in AFG procedures.

Methods

A 52-question survey was emailed to 3106 active members of The Aesthetic Society. Two hundred and ninety-three responses were recorded, representing a 9% response rate.

Results

We analyzed 288 responses. The most common AFG procedures were facial (38%), gluteal (34%), and breast (27%) augmentation. Preoperative antibiotics were used by 84.0% overall, with rates of 74.3%, 88.0%, and 92.7% in face, breast, and gluteal AFG, respectively. Lipoaspirate-antibiotic mixing was reported by 19.8%, mainly during gluteal AFG (46.9%), and less so in face (2.8%) and breast (8%) AFG. Notably, 46.9% of surgeons administered prolonged prophylaxis for 72 h or more. Tranexamic acid was utilized by 39.9% of the surveyed surgeons. Platelet-rich plasma was used by 5.6%. Doppler ultrasound was incorporated by 16.7% in AFG, with 21.5% in gluteal AFG, 14% in the face, and 19% in breast procedures.

Conclusions

In this survey, we offer insights into antibiotic practices and adjunct therapies in AFG, especially intraoperative antibiotic mixing. Practices among members of The Aesthetic Society vary from guidelines. It is crucial to standardize practices and conduct further research to pave the way for evidence-based guidelines in AFG.

Level of Evidence 5

Prevalence of Enteric Infections in Patients on Immune Checkpoint Inhibitors and Impact on Management and Outcomes

BACKGROUND

Stool pathogen testing is recommended as part of the initial evaluation for patients with new-onset diarrhea on immune checkpoint inhibitors (ICIs), yet its significance has not been well-studied. We aimed to determine the impact of multiplex gastrointestinal (GI) pathogen PCR testing on the clinical course and use of immunosuppressive therapy in patients who develop diarrhea on ICIs.

METHODS

This retrospective cohort included individuals who underwent GI pathogen panel PCR for diarrhea on ICIs at Memorial Sloan Kettering between 7/2015 and 7/2021. The primary outcome was use of immunosuppressive therapy for suspected immunotherapy-related enterocolitis (irEC). Secondary outcomes included diarrhea severity and endoscopic and histologic disease patterns.

RESULTS

Among 521 ICI-treated patients tested for GI pathogens, 61 (11.7%) had a positive PCR. Compared to patients without detectable infections, patients with infections had more frequent grades 3-4 diarrhea (37.7% vs. 19.6%, P < .01) and colitis (39.3% vs. 14.7%, P < .01). However, patients with infections did not have higher rates of persistent or recurrent diarrhea and were less likely to receive steroids (P < .01) and second-line immunosuppressive agents (P = .03). In 105 patients with lower endoscopy, similar trends were observed and no differences in endoscopic severity or histologic patterns were noted between groups.

CONCLUSIONS

GI infections in ICI-treated patients presenting with diarrhea are linked to more severe but self-limited clinical presentations and may be optimally treated with observation and supportive care alone. Routine and timely stool pathogen testing may help avert unnecessary empiric immunosuppression for suspected irEC, which has been linked to blunted antitumor responses and numerous adverse effects.

MetaNorm: incorporating meta-analytic priors into normalization of NanoString nCounter data

MOTIVATION

Non-informative or diffuse prior distributions are widely employed in Bayesian data analysis to maintain objectivity. However, when meaningful prior information exists and can be identified, using an informative prior distribution to accurately reflect current knowledge may lead to superior outcomes and great efficiency.

RESULTS

We propose MetaNorm, a Bayesian algorithm for normalizing NanoString nCounter gene expression data. MetaNorm is based on RCRnorm, a powerful method designed under an integrated series of hierarchical models that allow various sources of error to be explained by different types of probes in the nCounter system. However, a lack of accurate prior information, weak computational efficiency, and instability of estimates that sometimes occur weakens the approach despite its impressive performance. MetaNorm employs priors carefully constructed from a rigorous meta-analysis to leverage information from large public data. Combined with additional algorithmic enhancements, MetaNorm improves RCRnorm by yielding more stable estimation of normalized values, better convergence diagnostics and superior computational efficiency.

AVAILABILITY AND IMPLEMENTATION

R Code for replicating the meta-analysis and the normalization function can be found at github.com/jbarth216/MetaNorm.

Pectoral muscle removal in mammogram images: A novel approach for improved accuracy and efficiency

PURPOSE

Accurate pectoral muscle removal is critical in mammographic breast density estimation and many other computer-aided algorithms. We propose a novel approach to remove pectoral muscles form mediolateral oblique (MLO) view mammograms and compare accuracy and computational efficiency with existing method (Libra).

METHODS

A pectoral muscle identification pipeline was developed. The image is first binarized to enhance contrast and then the Canny algorithm was applied for edge detection. Robust interpolation is used to smooth out the pectoral muscle region. Accuracy and computational speed of pectoral muscle identification was assessed using 951 women (1,902 MLO mammograms) from the Joanne Knight Breast Health Cohort at Washington University School of Medicine.

RESULTS

Our proposed algorithm exhibits lower mean error of 12.22% in comparison to Libra's estimated error of 20.44%. This 40% gain in accuracy was statistically significant (p < 0.001). The computational time for the proposed algorithm is 5.4 times faster when compared to Libra (5.1 s for proposed vs. 27.7 s for Libra per mammogram).

CONCLUSION

We present a novel approach for pectoral muscle removal in mammogram images that demonstrates significant improvement in accuracy and efficiency compared to existing method. Our findings have important implications for the development of computer-aided systems and other automated tools in this field.

Software Application Profile: dynamicLM-a tool for performing dynamic risk prediction using a landmark supermodel for survival data under competing risks

MOTIVATION

Providing a dynamic assessment of prognosis is essential for improved personalized medicine. The landmark model for survival data provides a potentially powerful solution to the dynamic prediction of disease progression. However, a general framework and a flexible implementation of the model that incorporates various outcomes, such as competing events, have been lacking. We present an R package, dynamicLM, a user-friendly tool for the landmark model for the dynamic prediction of survival data under competing risks, which includes various functions for data preparation, model development, prediction and evaluation of predictive performance.

IMPLEMENTATION

dynamicLM as an R package.

GENERAL FEATURES

The package includes options for incorporating time-varying covariates, capturing time-dependent effects of predictors and fitting a cause-specific landmark model for time-to-event data with or without competing risks. Tools for evaluating the prediction performance include time-dependent area under the ROC curve, Brier Score and calibration.

AVAILABILITY

Available on GitHub [https://github.com/thehanlab/dynamicLM].

Exocrine Pancreatic Insufficiency Induced by Immune Checkpoint Inhibitors

BACKGROUND

Scant data describe exocrine pancreatic insufficiency (EPI) secondary to immune checkpoint inhibitor (ICI) use. The goal of this study is to describe the incidence, risk factors, and clinical characteristics of patients with ICI-related EPI.

PATIENTS AND METHODS

A single center, retrospective case-control study was performed of all ICI-treated patients at Memorial Sloan Kettering Cancer Center between January 2011 and July 2020. ICI-related EPI patients had steatorrhea with or without abdominal discomfort or weight loss, started pancrelipase after initiation of ICI, and demonstrated symptomatic improvement with pancrelipase. Controls were matched 2:1 by age, race, sex, cancer type, and year of ICI start.

RESULTS

Of 12 905 ICI-treated patients, 23 patients developed ICI-related EPI and were matched to 46 controls. The incidence rate of EPI was 1.18 cases per 1000 person-years and the median onset of EPI was 390 days after the first dose of ICI. All 23 (100%) EPI cases had steatorrhea that improved with pancrelipase, 12 (52.2%) had weight loss, and 9 (39.1%) had abdominal discomfort; none had changes of chronic pancreatitis on imaging. Nine (39%) EPI patients had episodes of clinical acute pancreatitis preceding the onset of EPI, compared to 1 (2%) control (OR 18.0 (2.5-789.0), P < .001). Finally, the EPI group exhibited higher proportions of new or worsening hyperglycemia after ICI exposure compared with the control group (9 (39.1%) vs. 3 (6.5%), P < .01).

CONCLUSION

ICI-related EPI is a rare but clinically significant event that should be considered in patients with late onset diarrhea after ICI treatment and often is associated with development of hyperglycemia and diabetes.

Shifting Sociodemographic Characteristics of a Phase I Clinical Trial Population at an NCI-Designated Comprehensive Cancer Center in the Southeast

Racial and ethnic minority populations are consistently under-represented in oncology clinical trials despite comprising a disproportionate share of a cancer burden. Phase I oncology clinical trials pose a unique challenge and opportunity for minority inclusion. Here we compared the sociodemographic characteristics of patients participating in phase 1 clinical trials a National Cancer Institute ( NCI)-designated comprehensive center to all patients at the center, patients with new cancer diagnosis in metropolitan Atlanta and patients with new cancer diagnoses in the state of Georgia. From 2015 to 2020, 2325 patients (43.4% female, 56.6% male) consented to participate in a phase I trial. Grouped self-reported race distribution was 70.3% White, 26.2% Black, and 3.5% other. Of new patient registrations at Winship Cancer Institute (N = 107 497) (50% F, 50% M), grouped race distribution was 63.3% White, 32.0% Black, and 4.7% other. Patients with new cancer diagnoses in metro Atlanta from 2015 to 2016 (N = 31101) were 58.4% White, 37.2% Black, and 4.3% other. Race and sex distribution of phase I patients was significantly different than Winship patients (P < .001). Over time, percent of White patients decreased in both phase I and Winship groups (P = .009 and P < .001, respectively); percentage of females did not change in either group (P = .54 phase I, P = .063 Winship). Although phase I patients were more likely to be White, male, and privately ensured than the Winship cohort, from 2015 to 2020 the percentage of White patients in phase I trials and among all new patients treated at Winship decreased. The intent of characterizing existing disparities is to improve the representation of patients from racial and ethnic minority backgrounds in phase I clinical trials.

Immune-Related Adverse Events and Clinical Outcomes in Advanced Urothelial Cancer Patients Treated With Immune Checkpoint Inhibitors

BACKGROUND

In advanced urothelial cancers (UC), immune checkpoint inhibitors (ICI) show promise as a durable therapy. Immune-related adverse events (irAEs), a side effect of ICIs, may serve as an indicator of beneficial response. We investigated the relationship between irAEs and clinical outcomes in patients with advanced UC who received ICI.

MATERIALS AND METHODS

In this retrospective study, we investigated 70 patients with advanced UC treated with ICIs at Winship Cancer Institute from 2015 to 2020. Data on patients were collected through chart review. Cox's proportional hazard model and logistic regression were applied to estimate the association with overall survival (OS), progression-free survival (PFS), and clinical benefit (CB). The possible lead-time bias was handled in extended Cox regression models.

RESULTS

The median age of the cohort was 68. Over one-third (35%) of patients experienced an irAE, with skin being the most frequent organ involved (12.9%). Patients that experienced at least one irAE had significantly enhanced OS (HR: 0.38, 95% CI, 0.18-0.79, P = .009), PFS (HR: 0.27, 95% CI, 0.14-0.53, P < .001), and CB (OR: 4.20, 95% CI, 1.35-13.06, P = .013). Patients who experienced dermatologic irAEs also had significantly greater OS, PFS, and CB.

CONCLUSION

Of patients with advanced UC that had undergone ICI therapy, those who had irAEs, especially dermatologic irAEs, had significantly greater OS, PFS, and CB. These results may suggest that irAE's may serve as an important marker of durable response to ICI therapy in urothelial cancer. The findings of this study need to be validated with larger cohort studies in the future.

Early Onset Colorectal Cancer: A Hypothesis

The rising rates of early onset colorectal cancer are perplexing. This commentary discusses what may be causing the increase.

Guanine-containing ssDNA and RNA induce dimeric and tetrameric structural forms of SAMHD1

The dNTPase activity of tetrameric SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1 (SAMHD1) plays a critical role in cellular dNTP regulation. SAMHD1 also associates with stalled DNA replication forks, DNA repair foci, ssRNA and telomeres. The above functions require nucleic acid binding by SAMHD1, which may be modulated by its oligomeric state. Here we establish in cryo-EM and biochemical studies that the guanine-specific A1 activator site of each SAMHD1 monomer is used to target the enzyme to guanine nucleotides within single-stranded (ss) DNA and RNA. Remarkably, nucleic acid strands containing a single guanine base induce dimeric SAMHD1, while two or more guanines with ∼20 nucleotide spacing induce a tetrameric form. A cryo-EM structure of ssRNA-bound tetrameric SAMHD1 shows how ssRNA strands bridge two SAMHD1 dimers and stabilize the structure. This ssRNA-bound tetramer is inactive with respect to dNTPase and RNase activity.

A Phase I Trial of Bevacizumab and Temsirolimus in Combination With Valproic Acid in Advanced Solid Tumors

BACKGROUND

Preclinical models suggest synergy between anti-angiogenesis therapy, mammalian target of rapamycin (mTOR), and histone deacetylase inhibitors to promote anticancer activity.

METHODS

This phase I study enrolled 47 patients between April 2012 and 2018 and determined safety, maximum tolerated dose (MTD), and dose-limiting toxicities (DLTs) when combining bevacizumab, temsirolimus, and valproic acid in patients with advanced cancer.

RESULTS

Median age of enrolled patients was 56 years. Patients were heavily pretreated with a median of 4 lines of prior therapy. Forty-five patients (95.7%) experienced one or more treatment-related adverse events (TRAEs). Grade 3 TRAEs were lymphopenia (14.9%), thrombocytopenia (8.5%), and mucositis (6.4%). Grade 4 TRAEs included lymphopenia (2.1%) and CNS cerebrovascular ischemia (2.1%). Six patients developed DLTs across 10 dose levels with grade 3 infection, rash, mucositis, bowel perforation, elevated lipase, and grade 4 cerebrovascular ischemia. The MTD was dose level 9 (bevacizumab 5 mg/kg days 1 and 15 intravenously (IV) plus temsirolimus 25 mg days 1, 8, 15, and 22 IV and valproic acid 5 mg/kg on days 1-7 and 15-21 per orally (PO)). Objective response rate (ORR) was 7.9% with confirmed partial response (PRs) in 3 patients (one each in parotid gland, ovarian, and vaginal cancers). Stable disease (SD) ≥+6 months was seen in 5 patients (13.1%). Clinical benefit state (CBR: PR + SD ≥+6 months) was 21%.

CONCLUSION

Combination therapy with bevacizumab, temsirolimus, and valproic acid was feasible, but there were numerous toxicities, which will require careful management for future clinical development (ClinicalTrials.gov Identifier: NCT01552434).

TATDN2 resolution of R-loops is required for survival of BRCA1-mutant cancer cells

BRCA1-deficient cells have increased IRE1 RNase, which degrades multiple microRNAs. Reconstituting expression of one of these, miR-4638-5p, resulted in synthetic lethality in BRCA1-deficient cancer cells. We found that miR-4638-5p represses expression of TATDN2, a poorly characterized member of the TATD nuclease family. We discovered that human TATDN2 has RNA 3' exonuclease and endonuclease activity on double-stranded hairpin RNA structures. Given the cleavage of hairpin RNA by TATDN2, and that BRCA1-deficient cells have difficulty resolving R-loops, we tested whether TATDN2 could resolve R-loops. Using in vitro biochemical reconstitution assays, we found TATDN2 bound to R-loops and degraded the RNA strand but not DNA of multiple forms of R-loops in vitro in a Mg2+-dependent manner. Mutations in amino acids E593 and E705 predicted by Alphafold-2 to chelate an essential Mg2+ cation completely abrogated this R-loop resolution activity. Depleting TATDN2 increased cellular R-loops, DNA damage and chromosomal instability. Loss of TATDN2 resulted in poor replication fork progression in the presence of increased R-loops. Significantly, we found that TATDN2 is essential for survival of BRCA1-deficient cancer cells, but much less so for cognate BRCA1-repleted cancer cells. Thus, we propose that TATDN2 is a novel target for therapy of BRCA1-deficient cancers.

A novel human papillomavirus and host DNA methylation score and detection of cervical adenocarcinoma

BACKGROUND

The widespread introduction of Pap testing in the 1960s was followed by substantial reductions in the incidence of cervical squamous cell cancer (SCC). However, the incidence of cervical adenocarcinoma (ADC) did not decrease, likely because of low Pap test sensitivity for ADC and adenocarcinoma in situ (AIS). This study assessed a novel human papillomavirus (HPV) and host DNA Methylation Score for AIS and ADC screening.

METHODS

We measured methylation levels at CpG sites in the L2/L1 open reading frames of HPV16, HPV18, and HPV45-as well as 2 human loci, DCC and HS3ST2. Specifically, we tested exfoliated cervicovaginal cells from women in the HPV Persistence and Progression (PaP) cohort who were positive for 1 of HPV16, 18, or 45, including: 1) 176 with AIS/ADC, 2) 353 with cervical intraepithelial neoplasia-3 (CIN3) or SCC, and 3) controls who either cleared (HPV-Clearers; n = 579) or had persistent HPV16, 18, or 45 infection (HPV-Persisters; n = 292). CpG site-specific methylation percentages were measured using our reported next-generation methods. The Methylation Score was the average methylation percentage across all 35 CpG sites tested.

RESULTS

Each individual CpG site had higher methylation percentages in exfoliated cervicovaginal cells collected from patients with AIS/ADC, and as well as those with CIN3/SCC, relative to either control group (weakest P  = .004). The Methylation Score for AIS/ADC had a sensitivity of 74% and specificity of 89%. The multivariate odds ratio (OR) between the Methylation Score (4th vs 1st quartile) for AIS/ADC was ORq4-q1 = 49.01 (PBenjamini-Hochberg = 4.64E-12), using HPV-Clearers as controls. CIN3/SCC had similar, albeit weaker, associations with the Methylation Score.

CONCLUSIONS

HPV16/18/45-infected women with Methylation Scores in the highest quartile had very high odds of AIS/ADC, suggesting they may warrant careful histologic evaluation of the cervical transition zone (eg, conization or loop electrosurgical excision procedure [LEEP]).

The National Cancer Institute's Cancer Disparities Research Partnership Program: a unique funding model 20 years later

The burden of cancer and access to effective treatment are not experienced equally by all in the United States. For underserved populations that often access the health-care system when their cancers are in advanced disease stages, radiation oncology services are essential. In 2001, the National Cancer Institute's (NCI's) Radiation Research Program created and implemented the Cancer Disparities Research Partnership Program (CDRP). CDRP was a pioneering funding model whose goal was to increase participation of medically underserved populations in NCI clinical trials. CDRP's Cooperative Agreement funding supported for awardees the planning, development, and conduct of radiation oncology clinical research in institutions not traditionally involved in NCI-sponsored research and cared for a disproportionate number of medically underserved, health-disparities populations. The awardee secured and provided support for mentorship from 1 of 2 NCI comprehensive cancer centers named in its application. Six CDRP awards were made over two 5-year funding periods ending in 2013, with the end-of-program accomplishments previously reported. With the current focus on addressing equity, diversity, and inclusion, the 6 principal investigators were surveyed, 5 of whom responded about the impact of CDRP on their institutions, communities, and personal career paths. The survey that was emailed included 10 questions on a 5-point Likert scale. It was not possible to collect patient data this long after completion of the program. This article provides a 20-year retrospective of the experiences and observations from those principal investigators that can inform those now planning, building, and implementing equity, diversity, and inclusion programs.

Developing and assessing a kin keeping scale with application to identifying central influencers in African American family networks

Promoting family communication about inherited disease risk is an arena in which family systems theory is highly relevant. One family systems' construct that can support promotion of family communication regarding inherited disease risk is the notion of "kin keeping." However, kin keeping and whether it might be capitalized on to encourage family communication about inherited risk has been understudied. The goal of this report was to propose a broadened conceptualization of kin keeping that distinguishes between a structural functional perspective (role conceptualization) and transitional behaviors (skill conceptualization), and to develop and evaluate a scale that would enable this assertion to be tested among a sample of African American community health workers. We developed a scale using four steps: item development using concept analysis and content validity, scale development among a national sample (n = 312), scale evaluation using exploratory factor analysis (n = 52), and scale reduction. We then posed suppositions of associations that would indicate whether the developed kin keeping measure was assessing a specific family role or set of behaviors. Our results included the development of the first quantitative measure of kin keeping (9- and 15-item scales). Model fit for 9-item scale (CFI = 0.97, AFGI = 0.89, RMSEA = 0.09, SMRM = 0.06) and model fit for 15-item scale (CFI = 0.97, AFGI = 0.89, RMSEA = 0.06, SMRM = 0.05). These findings allow us to move toward more rigorous research about the role of kin keeping on information sharing and health decision making. Results also suggest that, contrary to the historical structural functional conceptualization of kin keeping as a role, kin keeping might also be conceptualized as a behavior or set of modifiable behaviors. Ultimately, the kin keeping scale could be used to operationalize kin keeping in various theoretical models and frameworks, guide intervention development to encourage or train for kin keeping behaviors, and test assumptions of whether families vary in the density of kin keeping.

Comparison of cell response to chromatin and DNA damage

DNA-targeting drugs are widely used for anti-cancer treatment. Many of these drugs cause different types of DNA damage, i.e. alterations in the chemical structure of DNA molecule. However, molecules binding to DNA may also interfere with DNA packing into chromatin. Interestingly, some molecules do not cause any changes in DNA chemical structure but interfere with DNA binding to histones and nucleosome wrapping. This results in histone loss from chromatin and destabilization of nucleosomes, a phenomenon that we call chromatin damage. Although the cellular response to DNA damage is well-studied, the consequences of chromatin damage are not. Moreover, many drugs used to study DNA damage also cause chromatin damage, therefore there is no clarity on which effects are caused by DNA or chromatin damage. In this study, we aimed to clarify this issue. We treated normal and tumor cells with bleomycin, nuclease mimicking drug which cut predominantly nucleosome-free DNA and therefore causes DNA damage in the form of DNA breaks, and CBL0137, which causes chromatin damage without direct DNA damage. We describe similarities and differences between the consequences of DNA and chromatin damage. Both agents were more toxic for tumor than normal cells, but while DNA damage causes senescence in both normal and tumor cells, chromatin damage does not. Both agents activated p53, but chromatin damage leads to the accumulation of higher levels of unmodified p53, which transcriptional activity was similar to or lower than that of p53 activated by DNA damage. Most importantly, we found that while transcriptional changes caused by DNA damage are limited by p53-dependent activation of a small number of p53 targets, chromatin damage activated many folds more genes in p53 independent manner.

Mechanisms of Ovarian Cancer-Associated Cachexia

Cancer-associated cachexia occurs in 50% to 80% of cancer patients and is responsible for 20% to 30% of cancer-related deaths. Cachexia limits survival and treatment outcomes, and is a major contributor to morbidity and mortality during cancer. Ovarian cancer is one of the leading causes of cancer-related deaths in women, and recent studies have begun to highlight the prevalence and clinical impact of cachexia in this population. Here, we review the existing understanding of cachexia pathophysiology and summarize relevant studies assessing ovarian cancer-associated cachexia in clinical and preclinical studies. In clinical studies, there is increased evidence that reduced skeletal muscle mass and quality associate with worse outcomes in subjects with ovarian cancer. Mouse models of ovarian cancer display cachexia, often characterized by muscle and fat wasting alongside inflammation, although they remain underexplored relative to other cachexia-associated cancer types. Certain soluble factors have been identified and successfully targeted in these models, providing novel therapeutic targets for mitigating cachexia during ovarian cancer. However, given the relatively low number of studies, the translational relevance of these findings is yet to be determined and requires more research. Overall, our current understanding of ovarian cancer-associated cachexia is insufficient and this review highlights the need for future research specifically aimed at exploring mechanisms of ovarian cancer-associated cachexia by using unbiased approaches and animal models representative of the clinical landscape of ovarian cancer.

An automatic pipeline for PET/MRI attenuation correction validation in the brain

PURPOSE

Challenges in PET/MRI quantitative accuracy for neurological uses arise from PET attenuation correction accuracy. We proposed and evaluated an automatic pipeline to assess the quantitative accuracy of four MRI-derived PET AC methods using analytically simulated PET brain lesions and ROIs as ground truth for PET activity.

METHODS

Our proposed pipeline, integrating a synthetic lesion insertion tool and the FreeSurfer neuroimaging framework, inserts simulated spherical and brain ROIs into PET projection space, reconstructing them via four PET MRAC techniques. Utilizing an 11-patient brain PET dataset, we compared the quantitative accuracy of four MRACs (DIXON, DIXONbone, UTE AC, and DL-DIXON) against the gold standard PET CTAC, evaluating MRAC to CTAC activity bias in spherical lesions and brain ROIs with and without background activity against original (lesion free) PET reconstructed images.

RESULTS

The proposed pipeline yielded accurate results for spherical lesions and brain ROIs, adhering to the MRAC to CTAC pattern of original brain PET images. Among the MRAC methods, DIXON AC exhibited the highest bias, followed by UTE, DIXONBone, and DL-DIXON showing the least. DIXON, DIXONbone, UTE, and DL-DIXON showed MRAC to CTAC biases of - 5.41%, - 1.85%, - 2.74%, and 0.08% respectively for ROIs inserted in background activity; - 7.02%, - 2.46%, - 3.56%, and - 0.05% for lesion ROIs without background; and - 6.82%, - 2.08%, - 2.29%, and 0.22% for the original brain PET images' 16 FreeSurfer brain ROIs.

CONCLUSION

The proposed pipeline delivers accurate results for synthetic spherical lesions and brain ROIs, with and without background activity consideration, enabling the evaluation of new attenuation correction approaches without utilizing measured PET emission data. Additionally, it offers a consistent method to generate realistic lesion ROIs, potentially applicable in assessing further PET correction techniques.

ZNF432 stimulates PARylation and inhibits DNA resection to balance PARPi sensitivity and resistance

Zinc finger (ZNF) motifs are some of the most frequently occurring domains in the human genome. It was only recently that ZNF proteins emerged as key regulators of genome integrity in mammalian cells. In this study, we report a new role for the Krüppel-type ZNF-containing protein ZNF432 as a novel poly(ADP-ribose) (PAR) reader that regulates the DNA damage response. We show that ZNF432 is recruited to DNA lesions via DNA- and PAR-dependent mechanisms. Remarkably, ZNF432 stimulates PARP-1 activity in vitro and in cellulo. Knockdown of ZNF432 inhibits phospho-DNA-PKcs and increases RAD51 foci formation following irradiation. Moreover, purified ZNF432 preferentially binds single-stranded DNA and impairs EXO1-mediated DNA resection. Consequently, the loss of ZNF432 in a cellular system leads to resistance to PARP inhibitors while its overexpression results in sensitivity. Taken together, our results support the emerging concept that ZNF-containing proteins can modulate PARylation, which can be embodied by the pivotal role of ZNF432 to finely balance the outcome of PARPi response by regulating homologous recombination.

M2 isoform of pyruvate kinase rewires glucose metabolism during radiation therapy to promote an antioxidant response and glioblastoma radioresistance

BACKGROUND

Resistance to existing therapies is a significant challenge in improving outcomes for glioblastoma (GBM) patients. Metabolic plasticity has emerged as an important contributor to therapy resistance, including radiation therapy (RT). Here, we investigated how GBM cells reprogram their glucose metabolism in response to RT to promote radiation resistance.

METHODS

Effects of radiation on glucose metabolism of human GBM specimens were examined in vitro and in vivo with the use of metabolic and enzymatic assays, targeted metabolomics, and FDG-PET. Radiosensitization potential of interfering with M2 isoform of pyruvate kinase (PKM2) activity was tested via gliomasphere formation assays and in vivo human GBM models.

RESULTS

Here, we show that RT induces increased glucose utilization by GBM cells, and this is accompanied with translocation of GLUT3 transporters to the cell membrane. Irradiated GBM cells route glucose carbons through the pentose phosphate pathway (PPP) to harness the antioxidant power of the PPP and support survival after radiation. This response is regulated in part by the PKM2. Activators of PKM2 can antagonize the radiation-induced rewiring of glucose metabolism and radiosensitize GBM cells in vitro and in vivo.

CONCLUSIONS

These findings open the possibility that interventions designed to target cancer-specific regulators of metabolic plasticity, such as PKM2, rather than specific metabolic pathways, have the potential to improve the radiotherapeutic outcomes in GBM patients.

The Spectrum of Headache in Leptomeningeal Metastases: A Comprehensive Review with Clinical Management Guidelines

PURPOSE OF REVIEW

Headaches are a common, oftentimes debilitating symptom in patients with leptomeningeal metastases.

RECENT FINDINGS

The third edition of the International Classification of Headache Disorders provides a useful diagnostic framework for headaches secondary to leptomeningeal metastases based on the temporal relationship of headache with disease onset, change in headache severity in correlation with leptomeningeal disease burden, and accompanying neurologic signs such as cranial nerve palsies and encephalopathy. However, headaches in patients with leptomeningeal metastases can be further defined by a wide range of varying cancer- and treatment-related pathophysiologies, each requiring a tailored approach. A thorough review of the literature and expert opinion on five observed headache sub-classifications in patients with leptomeningeal metastases is provided, with attention to necessary diagnostic testing, recommended first-line treatments, and prevention strategies.

The current landscape of therapies for hepatocellular carcinoma

Globally, primary liver cancer is the third leading cause of cancer-related deaths, with approximately 830 000 deaths worldwide in 2020, accounting for 8.3% of total deaths from all cancer types (1). This disease disproportionately affects those in countries with low or medium Human Development Index scores in Eastern Asia, South-Eastern Asia, and Northern and Western Africa (2). Hepatocellular carcinoma (HCC), the most common type of primary liver cancer, often develops in the background of chronic liver disease, caused by hepatitis B or C virus, non-alcoholic steatohepatitis (NASH), or other diseases that cause cirrhosis. Prognosis can vary dramatically based on number, size, and location of tumors. Hepatic synthetic dysfunction and performance status (PS) also impact survival. The Barcelona Clinic Liver Cancer (BCLC) staging system best accounts for these variations, providing a reliable prognostic stratification. Therapeutic considerations of this complex disease necessitate a multidisciplinary approach and can range from curative-intent surgical resection, liver transplantation or image-guided ablation to more complex liver-directed therapies like transarterial chemoembolization (TACE) and systemic therapy. Recent advances in the understanding of the tumor biology and microenvironment have brought new advances and approvals for systemic therapeutic agents, often utilizing immunotherapy or VEGF-targeted agents to modulate the immune response. This review will discuss the current landscape in the treatments available for early, intermediate, and advanced stage HCC.

Cumulative incidence of anal cancer since HIV or AIDS diagnosis in the United States

Treatment of screen-detected anal high-grade squamous intraepithelial lesions has been shown to effectively reduce the incidence of invasive anal cancer in people with HIV. We provide population-based estimates of cumulative incidence of anal cancer by risk group and age at HIV or AIDS diagnosis. The 0- to 10-year cumulative incidence of anal cancer for men who have sex with men and are younger than 30 years of age at HIV diagnosis was 0.17% (95% confidence interval [CI] = 0.13% to 0.20%) compared with 0.04% (95% CI = 0.02% to 0.06%) in other men and 0.03% (95% CI = 0.01% to 0.04%) in women. For men who have sex with men and have a diagnosis of AIDS and are younger than 30 years of age, the 0- to 10-year cumulative incidence was 0.35% (95% CI = 0.28% to 0.41%). Among people with HIV, men who have sex with men are at the greatest risk of anal cancer, and those with a diagnosis of AIDS had higher risk than those without AIDS. These estimates may inform recommendations for priority populations that could benefit most from anal cancer screening and treatment.

Effect of chronic disease on racial difference in COVID-19-associated hospitalization among cancer patients

BACKGROUND

Research indicates that Black cancer patients have higher rates of COVID-19 hospitalization than their White counterparts. However, the extent to which chronic diseases contribute to racial disparities remains uncertain. We aimed to quantify the effect of chronic diseases on racial disparity in COVID-19-associated hospitalization among cancer patients.

METHODS

We linked Louisiana Tumor Registry's data with statewide COVID-19 data and hospital in-patient discharge data to identify patients diagnosed with cancer in 2015-2019 who tested positive for COVID-19 in 2020 and those with COVID-19-associated hospitalization. Multivariable logistic regression and mediation methods based on linear structural equations were employed to assess the effects of the number of chronic diseases (0, 1-2, ≥3) and individual chronic diseases.

RESULTS

Of 6381 cancer patients who tested positive for COVID-19, 31.6% were non-Hispanic Black cancer patients. Compared with non-Hispanic White cancer patients, non-Hispanic Black cancer patients had a higher prevalence of chronic diseases (79.5% vs 66.0%) and higher COVID-19-associated hospitalization (27.2% vs 17.2%). The odds of COVID-19-associated hospitalization were 80% higher for non-Hispanic Black cancer patients than non-Hispanic White cancer patients (odds ratio = 1.80, 95% confidence interval = 1.59 to 2.04). After adjusting for age, sex, insurance, poverty, obesity, and cancer type, number of chronic diseases explained 37.8% of the racial disparity in COVID-19-associated hospitalization, and hypertension, diabetes, and chronic renal disease were the top 3 chronic diseases explaining 9.6%, 8.9%, and 7.3% of the racial disparity, respectively.

CONCLUSION

Chronic diseases played a substantial role in the racial disparity in COVID-19-associated hospitalization among cancer patients, especially hypertension, diabetes, and renal disease. Understanding and addressing the root causes are crucial for targeted interventions, policies, and health-care strategies to reduce racial disparity.

Sepsis leads to lasting changes in phenotype and function of naïve CD8 T cells

Sepsis, an amplified immune response to systemic infection, is characterized by a transient cytokine storm followed by chronic immune dysfunction. Consequently, sepsis survivors are highly susceptible to newly introduced infections, suggesting sepsis can influence the function and composition of the naïve CD8 T cell pool and resulting pathogen-induced primary CD8 T cell responses. Here, we explored the extent to which sepsis induces phenotypic and functional changes within the naïve CD8 T cell pool. To interrogate this, the cecal ligation and puncture (CLP) mouse model of polymicrobial sepsis was used. In normal, non-septic mice, we show type-I interferon (IFN I)-mediated signaling plays an important role in driving the phenotypic and functional heterogeneity in the naïve CD8 T cell compartment leading to increased representation of Ly6C+ naïve CD8 T cells. In response to viral infection after sepsis resolution, naïve Ly6C+ CD8 T cells generated more primary effector and memory CD8 T cells with slower conversion to a central memory CD8 T cell phenotype (Tcm) than Ly6C- naïve CD8 T cells. Importantly, as a potent inducer of cytokine storm and IFN I production, sepsis leads to increased representation of Ly6C+ naïve CD8 T cells that maintained their heightened ability to respond (i.e., effector and memory CD8 T cell accumulation and cytokine production) to primary LCMV infection. Lastly, longitudinal analyses of peripheral blood samples obtained from septic patients revealed profound changes in CD8 T cell subset composition and frequency compared to healthy controls. Thus, sepsis has the capacity to alter the composition of naïve CD8 T cells, directly influencing primary CD8 T cell responses to newly introduced infections.

A workflow to study mechanistic indicators for driver gene prediction with Moonlight

Prediction of driver genes (tumor suppressors and oncogenes) is an essential step in understanding cancer development and discovering potential novel treatments. We recently proposed Moonlight as a bioinformatics framework to predict driver genes and analyze them in a system-biology-oriented manner based on -omics integration. Moonlight uses gene expression as a primary data source and combines it with patterns related to cancer hallmarks and regulatory networks to identify oncogenic mediators. Once the oncogenic mediators are identified, it is important to include extra levels of evidence, called mechanistic indicators, to identify driver genes and to link the observed gene expression changes to the underlying alteration that promotes them. Such a mechanistic indicator could be for example a mutation in the regulatory regions for the candidate gene. Here, we developed new functionalities and released Moonlight2 to provide the user with a mutation-based mechanistic indicator as a second layer of evidence. These functionalities analyze mutations in a cancer cohort to classify them into driver and passenger mutations. Those oncogenic mediators with at least one driver mutation are retained as the final set of driver genes. We applied Moonlight2 to the basal-like breast cancer subtype, lung adenocarcinoma and thyroid carcinoma using data from The Cancer Genome Atlas. For example, in basal-like breast cancer, we found four oncogenes (COPZ2, SF3B4, KRTCAP2 and POLR2J) and nine tumor suppressor genes (KIR2DL4, KIF26B, ARL15, ARHGAP25, EMCN, GMFG, TPK1, NR5A2 and TEK) containing a driver mutation in their promoter region, possibly explaining their deregulation. Moonlight2R is available at https://github.com/ELELAB/Moonlight2R.

A mathematical investigation of polyaneuploid cancer cell memory and cross-resistance in state-structured cancer populations

The polyaneuploid cancer cell (PACC) state promotes cancer lethality by contributing to survival in extreme conditions and metastasis. Recent experimental evidence suggests that post-therapy PACC-derived recurrent populations display cross-resistance to classes of therapies with independent mechanisms of action. We hypothesize that this can occur through PACC memory, whereby cancer cells that have undergone a polyaneuploid transition (PAT) reenter the PACC state more quickly or have higher levels of innate resistance. In this paper, we build on our prior mathematical models of the eco-evolutionary dynamics of cells in the 2N+ and PACC states to investigate these two hypotheses. We show that although an increase in innate resistance is more effective at promoting cross-resistance, this trend can also be produced via PACC memory. We also find that resensitization of cells that acquire increased innate resistance through the PAT have a considerable impact on eco-evolutionary dynamics and extinction probabilities. This study, though theoretical in nature, can help inspire future experimentation to tease apart hypotheses surrounding how cross-resistance in structured cancer populations arises.